Alignments for a candidate for glpK in Clostridium tyrobutyricum FAM22553

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Clostridium tyrobutyricum FAM22553

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_017752631.1 PN53_RS13255 glycerol kinase GlpK

Query= SwissProt::O66131
         (496 letters)



>NCBI__GCF_000816635.1:WP_017752631.1
          Length = 497

 Score =  668 bits (1724), Expect = 0.0
 Identities = 316/495 (63%), Positives = 389/495 (78%), Gaps = 1/495 (0%)

Query: 1   MNQYMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIA 60
           M +Y++A+DQGTTSSR I+FN+ G  V  +QKEF Q +P+ GWVEH+  EIW +   V  
Sbjct: 1   MAKYVMALDQGTTSSRCIIFNENGLPVSTSQKEFKQIYPEGGWVEHDPMEIWATQFGVAT 60

Query: 61  SVLSEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYD 120
             L ++ +K E +  IGITNQRETT+VW++ TG P+YNAIVWQ R+TA  CDELKAKG D
Sbjct: 61  ETLLKSNIKAEDIEAIGITNQRETTIVWDRRTGLPVYNAIVWQCRRTADYCDELKAKGVD 120

Query: 121 PLFRKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVT 180
            + ++KTGL++DAYFS TK+KWILD+V  AR  A RG L+FGT+DTWL+W L+ G+VHVT
Sbjct: 121 KIIKEKTGLVLDAYFSATKIKWILDNVPTARREANRGNLIFGTVDTWLMWNLTKGKVHVT 180

Query: 181 DYSNASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAG 240
           DY+NASRT++FNIH L+WD ELL++  +P++MLPEV+PSS VY + A    FGVE+PIAG
Sbjct: 181 DYTNASRTMLFNIHELKWDKELLELFDIPESMLPEVKPSSCVYGQAAE-SLFGVEIPIAG 239

Query: 241 AAGDQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYA 300
            AGDQQAALFGQ CF  GMAKNTYGTGCF+LMNTG+KAV SK+GLLTTIA GIDGKVEYA
Sbjct: 240 DAGDQQAALFGQTCFKPGMAKNTYGTGCFLLMNTGDKAVESKNGLLTTIAIGIDGKVEYA 299

Query: 301 LEGSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVR 360
           LEGSIF+ G++IQWLRD LRM+KTA +SE Y + VE T GVY+VPAF+GLG PYWD   R
Sbjct: 300 LEGSIFIGGASIQWLRDELRMLKTAPESEKYCDAVEDTGGVYLVPAFVGLGAPYWDQYAR 359

Query: 361 GAVFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLMQF 420
           G + G+TRGT KEHF+RAT+ESLAYQT DVL  ME DS I L  L+VDGGA  NNFLMQF
Sbjct: 360 GIMIGITRGTKKEHFVRATVESLAYQTYDVLKAMEEDSHIELKALKVDGGACANNFLMQF 419

Query: 421 QSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRTM 480
           QSD+L V V+RP V ETTALGAAYLAG+AVGYW +R+D+   W + + F P M +DKR  
Sbjct: 420 QSDILNVQVDRPKVIETTALGAAYLAGIAVGYWQNREDVRKNWAISKNFMPVMKEDKREK 479

Query: 481 LYDGWKKAVRAAMAF 495
           L +GW  AV+ +M +
Sbjct: 480 LLEGWHDAVKRSMGW 494


Lambda     K      H
   0.319    0.134    0.406 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 782
Number of extensions: 24
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 496
Length of database: 497
Length adjustment: 34
Effective length of query: 462
Effective length of database: 463
Effective search space:   213906
Effective search space used:   213906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_017752631.1 PN53_RS13255 (glycerol kinase GlpK)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01311.hmm
# target sequence database:        /tmp/gapView.72232.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01311  [M=496]
Accession:   TIGR01311
Description: glycerol_kin: glycerol kinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-235  767.2   0.7   3.1e-235  767.1   0.7    1.0  1  NCBI__GCF_000816635.1:WP_017752631.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_017752631.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  767.1   0.7  3.1e-235  3.1e-235       1     496 []       3     494 ..       3     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 767.1 bits;  conditional E-value: 3.1e-235
                             TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 
                                           k+++a+DqGttssr+i+f+++g  v+++qke++qi+p+ gwvEhdp+ei++++  v++e+l k++ikae+i+a
  NCBI__GCF_000816635.1:WP_017752631.1   3 KYVMALDQGTTSSRCIIFNENGLPVSTSQKEFKQIYPEGGWVEHDPMEIWATQFGVATETLLKSNIKAEDIEA 75 
                                           69*********************************************************************** PP

                             TIGR01311  74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146
                                           iGitnqREtt+vWd++tg p++naivWq++rta++++elk+++ ++ ++ektGL+l++YfsatK++W+ldnv+
  NCBI__GCF_000816635.1:WP_017752631.1  76 IGITNQRETTIVWDRRTGLPVYNAIVWQCRRTADYCDELKAKGVDKIIKEKTGLVLDAYFSATKIKWILDNVP 148
                                           ************************************************************************* PP

                             TIGR01311 147 evrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirssse 219
                                           ++r++a++g+l+fGtvdtwl+++Lt+gkvhvtd+tNASRt+l+n+++lkwd+ellelf+ip+++lPe+++ss 
  NCBI__GCF_000816635.1:WP_017752631.1 149 TARREANRGNLIFGTVDTWLMWNLTKGKVHVTDYTNASRTMLFNIHELKWDKELLELFDIPESMLPEVKPSSC 221
                                           ************************************************************************* PP

                             TIGR01311 220 vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklg 292
                                           vyg+ +e+ l++ e+pi+g +Gdqqaal+gq+c+k+g+aKntYgtGcFll+ntG+k+v sk+glLtt+a  ++
  NCBI__GCF_000816635.1:WP_017752631.1 222 VYGQAAES-LFGVEIPIAGDAGDQQAALFGQTCFKPGMAKNTYGTGCFLLMNTGDKAVESKNGLLTTIAIGID 293
                                           ******99.**************************************************************** PP

                             TIGR01311 293 gkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivG 365
                                           gk    yalEGs++++Ga +qwlrd+l+++k+a e+ek++ +ved++gvy+VPaf GL+aPyWd+ Arg+++G
  NCBI__GCF_000816635.1:WP_017752631.1 294 GKVE--YALEGSIFIGGASIQWLRDELRMLKTAPESEKYCDAVEDTGGVYLVPAFVGLGAPYWDQYARGIMIG 364
                                           9885..******************************************************************* PP

                             TIGR01311 366 ltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438
                                           +tr+t+keh++ra++e++a+q+ d+l+ame+d+++e+k+LkvDGg+++nn+lmq+q+dil+v+v rpkv ett
  NCBI__GCF_000816635.1:WP_017752631.1 365 ITRGTKKEHFVRATVESLAYQTYDVLKAMEEDSHIELKALKVDGGACANNFLMQFQSDILNVQVDRPKVIETT 437
                                           ************************************************************************* PP

                             TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           alGaA++ag+avg+w++ e+++k+++ + k+f p m+e++rek ++ w++av+rs++w
  NCBI__GCF_000816635.1:WP_017752631.1 438 ALGAAYLAGIAVGYWQNREDVRKNWAIS-KNFMPVMKEDKREKLLEGWHDAVKRSMGW 494
                                           ***************************7.***************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (497 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.41
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources